模块帮助文档

原始数据质控

fastq数据统计　FASTQ Summary Statistics

原始数据碱基分布图　Draw nucleotides distribution chart

原始数据质量分布图　Draw quality score boxplot

SE数据去接头、低质量　Trimmomatic SE(single-end)

PE数据去接头、低质量　Trimmomatic PE(paired-end)

fastq转fasta文件　Convert FASTQ to FASTA

计算fasta序列长度　Compute sequence length

按长度过滤fasta序列　ilter sequences by length

fasta序列统计　Fasta Statistics

BWA比对

构建参考序列BWA比对索引　BWA reference index

BWA比对，aln方法　Map with BWA

BWA比对，mem方法　Map with BWA-MEM

SAM/BAM工具

• SAM文件转BAM文件　SAM-to-BAM

• BAM文件转SAM文件   BAM-to-SAM

• 过滤BAM比对结果文件　Filter BAM

• BAM文件排序　Sort BAM

• 统计BAM比对结果　BAM Flagstat

• 统计BAM具体比对信息　BAM IdxStats

• 去除PCR Duplications    BAM RmDup

• 合并排序后的BAM文件　Merge sorted BAM Files

• GATK方法统计目标区域深度覆盖度　GATK DepthOfCoverage

• 目标区域深度统计　read depth per BED region

• 目标区域覆盖度统计　read coverage per BED region

变异检测和注释

• SNP/InDels Caller，变异检测　GATK Unified Genotyper

• 过滤VCF文件　Filter VCF File

• V2版本过滤VCF文件　Filter VCF File V2

• 变异检测结果注释　Annotate Variation

• V2版本变异检测结果注释　Annotate Variation V2

• V3版本变异检测结果注释　Annotate Variation V3

• 变异检测结果统计　Statistics Variation Information

目标区域处理工具

• 目标区域序列提取　Extract DNA sequences

• VCF文件坐标还原　VCF Restore Coordinate

• SAM文件坐标还原　SAM Restore Coordinate

BSA分析

• Clean VCF file for BSA Analysis

• Retain variants in VCF file

• I. SNP-Index Calculation

• II. SNP-Index Calculation

• Plot SNP-index from the beginning to the end in chromosome

• Get candidate region

• Get candidate region variants